Over the next three and one-half years, Theodore Roosevelt made 15 more deterrent patrols from the Holy Loch. Late in the spring of 1965, she departed Holy Loch on her 17th and final patrol of the deployment to Holy Loch. She concluded that patrol and the deployment when she arrived in Charleston on 15 June 1965. She unloaded her 16 Polaris missiles and then departed Charleston for New London, Connecticut, where she arrived on 26 June 1965.

At New London, Theodore Roosevelt entered the shipyard of the Electric Boat Division for an extensive overhaul. Between July 1965 and January 1967, her nuclear reactor was refueled and her Polaris weapon system was modified to accept the more advanced Polaris A3 missile. She completed overhaul on 14 January 1967 and began sea trials and refresher training, all of which culminated in the successful firing of a Polaris A3 missile at the Cape Canaveral missile range late in April 1967. At the end of the training period, she returned to Charleston to load missiles and to prepare for another series of deterrent patrols out of Holy Loch. She embarked upon her 18th patrol on 1 June 1967 and completed that cruise at the Holy Loch base.

Theodore Roosevelt's second tour of duty operating from the Scotland base proved to be very brief in comparison to her first. Between mid-June 1967 and February 1968, she completed her 18th through 21st patrols. On 20 March 1968 while returning to Holy Loch from her 21st patrol, she ran aground off the western coast of Scotland. After drydocking for temporary correction of the damage, she departed Holy Loch on 5 April 1968 to return to the United States for permanent repairs. Between 18 April and 20 April 1968 she unloaded her missiles at Charleston and headed north to New London. On 23 April 1968, she arrived in the shipyard of the Electric Boat Division and commenced an extended repair period. Labor disputes caused delays, and Theodore Roosevelt did not complete her repairs until mid-October 1968. She spent the latter part of that month in sea trials and then departed New London on 2 November 1968 on her post-repair shakedown cruise. She visited Norfolk, Virginia, Puerto Rico, and St. Croix in the United States Virgin Islands before concluding the cruise at Charleston on 27 November 1968. She conducted training operations out of Charleston before deploying to Holy Loch again early in 1969.

That tour of duty lasted until May 1971. During the interim, Theodore Roosevelt conducted nine more deterrent patrols, returning to Holy Loch for refit after each. On 12 May 1971, she stood out of Holy Loch on the 31st patrol of her career. On 20 July 1971, she arrived in New London completing both the patrol and the Holy Loch deployment. She remained in New London for three weeks, during which time members of her Blue crew and her Gold crew were brought together into a single overhaul crew while other members of both crews moved on to other assignments. On 10 August 1971, she headed south to Charleston where she arrived on 13 August 1971. Over the next month, she underwent refit and then departed Charleston on 11 September 1971 for special operations. Theodore Roosevelt returned to Charleston on 30 September 1971 and remained there a week and a day before returning to sea for another three weeks of special operations. She reentered Charleston on 1 November 1971 and began preoverhaul restricted repairs. Three weeks later, she officially began her refueling overhaul, which lasted for more than two years.

Theodore Roosevelt completed her overhaul in January 1974. During the following two months, she conducted sea trials out of Charleston. In April and May shakedown training and nuclear weapons certification preparations occupied her time. In June, she conducted a one-week United States Naval Academymidshipman familiarization cruise out of New London, then underwent nuclear propulsion safety training before deperming[clarification needed] at Norfolk. In mid-June, she received word of her reassignment to the United States Pacific Fleet with her new home port to be Pearl Harbor, Hawaii. Between July and September 1974, Theodore Roosevelt conducted another midshipman training cruise; then settled into pre-deployment training and preparations. She departed Charleston on 20 September 1974, transited the Panama Canal on 5 October, and, after a nine-day stop for missile load-out at Strategic Weapons Facility, Pacific in Bangor, Washington, continued on to Pearl Harbor, where she arrived on 4 November 1974. On 10 November, she departed Pearl Harbor, bound for the Mariana Islands. She entered port at Guam on 24 November, underwent refit at her new advanced base there, and began her first deterrent patrol in the Pacific Ocean on 31 December 1974.

Theodore Roosevelt conducted patrols out of Apra Harbor, Guam with support from the USS Proteus (AS-19) until beginning her last patrol (Patrol 46) on 9 October 1978, which ended in Pearl Harbor. Upon arrival in Pearl Harbor, a new crew was formed from members of the former Blue and Gold crews. From November 1978 until October 1979, Theodore Roosevelt served as a "target of opportunity" for various ASW forces including ships, aircraft and submarines. During this period she made several port calls to Lahaina, Maui, Kona, Hawaii, and Nawiliwili, Kuai. On 16 October 1979, the ship got underway for San Diego, California, arriving on 25 October. She transited from San Diego to Alameda from 29 October to 31 October. On 7 November, Theodore Roosevelt transited from Alameda to Esquimalt, British Columbia, arriving on 10 November. On 14 November, the ship left Esquimalt and arrived at Carr Inlet, Washington for acoustic testing while suspended on cables. On 19 November, she transited to Bangor, Washington and submitted the first official work request (2-Kilo) to the Trident Refit Facility. In December, she became the first boomer to offload her missiles at the newly-built Explosives Handling Wharf. She was the "First to do it last."[citation needed]